Structural characterizations of nonpeptidic thiadiazole inhibitors of matrix metalloproteinases reveal the basis for stromelysin selectivity

Abstract

The binding of two 5-substituted-l,3,4-thiadiazole-2-thione inhibitors to the matrix metalloproteinase stromelysin (MMP-3) have been characterized by protein crystallography. Both inhibitors coordinate to the catalytic zinc cation via an exocyclic sulfur and lay in an unusual position across the unprimed (Pl-P3) side of the proteinase active site. Nitrogen atoms in the thiadiazole moiety make specific hydrogen bond interactions with enzyme structural elements that are conserved across all enzymes in the matrix metalloproteinase class. Strong hydrophobic interactions between the inhibitors and the side chain of tyrosine-I55 appear to be responsible for the very high selectivity of these inhibitors for stromelysin. In these enzymehnhibitor complexes, the S 1 ' enzyme subsite is unoccupied. A conformational rearrangement of the catalytic domain occurs that reveals an inherent flexibility of the substrate binding region leading to speculation about a possible mechanism for modulation of stromelysin activity and selectivity.

Similarity of Binding Sites of Human Matrix Metalloproteinases

“…Subsite S1Ј exhibits the highest levels of similarity, followed by S2 and S3Ј subsites. The results add to multiple experimental proofs of flexibility of S1Ј subsite (12)(13)(14)(15)(16)(17)(18), help explain cases where desired specificity was not achieved upon optimization of groups fitting into S1Ј subsite (10,11), and contradict the view of S1Ј subsite as the specificity pocket of MMPs that is based on variability of rigid x-ray structures.…”

“…1). The probe was placed in each of the grid points, and the interaction energy was calculated with the partially flexible binding site in order to account for experimentally observed induced fit (12)(13)(14)(15)(16)(17). The approach also optimizes the backbone parts of amino acids, in contrast to a previous study (23) where only the side chains were movable.…”

“…Traditionally, S1Ј subsite (5) has been labeled as the specificity pocket (6, 7) because of its significant size and shape differences among the rigid x-ray structures of various MMPs. However, modifications of P1Ј part of the ligands led to both increased selectivity (8,9) and failures (10,11) that were explained by observed changes in the structure of the pocket upon inhibitor binding (12)(13)(14)(15)(16)(17)(18). The importance of other parts of the binding site, especially the unprimed side (11, 19 -21), for the design of more potent and selective inhibitors has been demonstrated as well.…”

Characterization of the Monomeric and Dimeric Forms of Latent and Active Matrix Metalloproteinase-9

“…This raises the question: why is the k cat value for the activation of pro-MMP-9 so low? The crystal structure of the catalytic domain of stromelysin 1 indicates that the active site is an extended cleft (43,49,50). Proteases generally prefer unstructured peptides as substrates.…”

<strong>Microwave-assisted Facile Synthesis And Anticancer Evaluation Of N-((5-(substituted Methylene Amino)- 1,3,4-thiadiazol-2-yl)methyl) Benzamide Derivatives</strong>

“…A separate well containing 0.01% DMSO only was run as DMSO control, which was found inactive under applied conditions. The cell growth was determined using MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (Sigma) reduction assay, which is based on ability of viable cells to reduce a soluble yellow tetrazolium salt to blue farmazan crystal [22,23]. Briefly, after 48 h of treatments, the10µl of MTT dye, prepared in phosphate buffered saline (PBS) were added to all wells.…”